I wanted to use custom repository for both cloudera manager and CDH. While adding a cluster/hosts there is an option to specify the URL pointing to custom CM repository (the page where we need to choose between parcel and package type installation). Based on this entry it creates an entry under /etc/apt/source.list.d folder.
But there is no option to add the CDH repository anywhere. I found that cloudera manager creates a file named cloudera-cdh5.list under /etc/apt/source.list.d with the following content (in my case)